Primer extension reactions are widely used in modern molecular biology. For example, in Sanger sequencing, an oligonucleotide primer is annealed to a 5′ end of a template, and deoxyribonucleotide triphosphates (dNTPs), polymerase, and four dideoxynucleotide terminators are added to form a reaction composition (the four teminators are either added to separate reactions or together in one reaction), and the reaction composition is incubated under appropriate conditions to achieve primer extension and termination.
Analysis of microsatellites, including Variable Number of Tandem Repeats (VNTRs) and Short Tandem Repeats (STRs), is another widely used method employing a primer extension reaction. STRs are sequences of two to seven nucleotides that are tandemly repeated at one or more locations in the genome. The number of tandem repeats varies from individual to individual. For certain genetic analysis techniques, STRs are amplified by PCR using specific primers flanking the repeat region and the number of repeats is determined. In certain techniques, the determination is made using size differentiation, e.g., by electrophoresis, mass spectroscopy, or chromatography.